Why did Jacob tell Joseph that Joseph’s first two sons, who were born while he was in Egypt, would be “called by his name”, but not the other sons?

The relevant passage is Genesis 48:5-6:

And now your two sons, who were born to you in the land of Egypt before I came to you in Egypt, are mine; Ephraim and Manasseh shall be mine, as Reuben and Simeon are.  (6)  And the children that you fathered after them shall be yours. They shall be called by the name of their brothers in their inheritance.

Joseph took the place of the firstborn among Jacob’s sons.  The actual firstborn, Reuben, had forfeited this privileged position because of his crime.   1 Chron 5:1-2:

The sons of Reuben the firstborn of Israel (for he was the firstborn, but because he defiled his father’s couch, his birthright was given to the sons of Joseph the son of Israel, so that he could not be enrolled as the oldest son;  (2)  though Judah became strong among his brothers and a chief came from him, yet the birthright belonged to Joseph)

So when Jacob blessed his sons, Joseph inherited the firstborn’s blessing of the double portion through the blessings given to his two sons, Manasseh and Ephraim.  These blessings given by Jacob, were obviously prophetic and had great meaning.  The two boys became 2 of the tribes in Israel.  Any other sons that Joseph would have (none are recorded) would not be part of this prophetic blessing given to Ephraim and Manasseh – they would not have the great blessing of heading a tribe in Israel, but would be included in the inheritance given to their brothers Ephraim and Manasseh.

We read how Manasseh and Ephraim would carry on the name of  Abraham, Isaac and Jacob in Genesis 48:15-16:

And he blessed Joseph and said, “The God before whom my fathers Abraham and Isaac walked, the God who has been my shepherd all my life long to this day,  (16)  the angel who has redeemed me from all evil, bless the boys; and in them let my name be carried on, and the name of my fathers Abraham and Isaac; and let them grow into a multitude in the midst of the earth.”

The tribes of Ephraim and Manasseh truly did grow into a multitude.  Joshua 17:14-18:

 Then the people of Joseph spoke to Joshua, saying, “Why have you given me but one lot and one portion as an inheritance, although I am a numerous people, since all along the LORD has blessed me?”  (15)  And Joshua said to them, “If you are a numerous people, go up by yourselves to the forest, and there clear ground for yourselves in the land of the Perizzites and the Rephaim, since the hill country of Ephraim is too narrow for you.”  (16)  The people of Joseph said, “The hill country is not enough for us. Yet all the Canaanites who dwell in the plain have chariots of iron, both those in Beth-shean and its villages and those in the Valley of Jezreel.”  (17)  Then Joshua said to the house of Joseph, to Ephraim and Manasseh, “You are a numerous people and have great power. You shall not have one allotment only,  (18)  but the hill country shall be yours, for though it is a forest, you shall clear it and possess it to its farthest borders. For you shall drive out the Canaanites, though they have chariots of iron, and though they are strong.”

So there was an allotment for both Ephraim and Manasseh west of the Jordan — in addition to the allotment given to Manasseh east of the Jordan by Moses.  Joshua 13:29-31:

And Moses gave an inheritance to the half-tribe of Manasseh. It was allotted to the half-tribe of the people of Manasseh according to their clans.  (30)  Their region extended from Mahanaim, through all Bashan, the whole kingdom of Og king of Bashan, and all the towns of Jair, which are in Bashan, sixty cities,  (31)  and half Gilead, and Ashtaroth, and Edrei, the cities of the kingdom of Og in Bashan. These were allotted to the people of Machir the son of Manasseh for the half of the people of Machir according to their clans.

If you look at a map of the allocations of land to the 12 tribes, you see very clearly that  Manasseh and Ephraim had a very large inheritance, right in the middle of everything.  As Jacob’s blessing said: “let them grow into a multitude in the midst of the earth”.

It also seems that when lists of the tribes are given, when Levi is included in the list, Joseph is used instead of Ephraim and Manasseh.  Conversely, when Ephraim and Manasseh are listed, Levi is omitted, thus keeping the tribes of Israel mentioned, to 12.